BN1934 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 1.2657e-04 9.1223e-04
Layer 5 1.3455e-04 1.9679e-03
Layer 3 6.8740e-04 1.7670e-02
Layer 6 8.8761e-04 9.2040e-03
WM 3.1674e-03 1.9333e-01
Layer 2 7.5503e-03 8.7731e-02
Layer 1 4.9695e-01 4.4232e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 5 2.5176 0.6806
PPIA Layer 4 2.2578 0.6217
EEF2 Layer 5 2.4023 0.6188
NORAD Layer 4 2.2578 0.6139
SYP Layer 4 2.6777 0.6103
PFKP Layer 5 2.5391 0.6049
ENO2 Layer 4 2.6777 0.6046
MORF4L1 Layer 5 2.4863 0.6045
TUBA1B Layer 5 2.2363 0.6037
KIF1A Layer 4 2.5391 0.6032
COX6C Layer 5 2.2676 0.6027
SEZ6L2 Layer 4 2.5176 0.6001
SNRPN Layer 4 2.6543 0.5990
DCLK1 Layer 5 2.4121 0.5987
COX6A1 Layer 3 2.1875 0.5986
APP Layer 5 2.3125 0.5974
TMSB10 Layer 5 2.2070 0.5962
UBC Layer 5 2.2773 0.5958
SLC24A2 Layer 4 2.3867 0.5946
HSP90AA1 Layer 5 2.1016 0.5929
SERINC1 Layer 5 2.3086 0.5928
COX4I1 Layer 5 2.1016 0.5910
PKM Layer 4 2.4844 0.5879
ATP6V1E1 Layer 4 2.3809 0.5878
RTN3 Layer 5 2.4512 0.5875
STMN1 Layer 4 2.5723 0.5874
NDRG4 Layer 5 2.6367 0.5862
GPI Layer 4 2.4941 0.5859
AP2M1 Layer 5 2.3711 0.5850
ARF1 Layer 4 2.5566 0.5848
PRKAR1B Layer 4 2.6426 0.5848
SH3GL2 Layer 4 2.6660 0.5843
SLC25A22 Layer 5 2.2363 0.5838
APLP2 Layer 4 2.2422 0.5837
GAPDH Layer 5 2.0586 0.5833
UBB Layer 5 2.2266 0.5832
YWHAG Layer 4 2.9219 0.5832
RPL9 Layer 4 2.0723 0.5830
MTCH1 Layer 5 2.2998 0.5823
STMN3 Layer 4 2.2930 0.5823
ATP6V0C Layer 5 2.4297 0.5816
WBP2 Layer 5 2.2715 0.5813
SYT1 Layer 4 2.7598 0.5813
CABP1 Layer 4 2.5566 0.5797
NUDT4 Layer 4 2.5273 0.5795
MAP4 Layer 4 2.4512 0.5795
RPH3A Layer 4 2.9023 0.5793
PPP2R1A Layer 4 2.4297 0.5781
EIF1 Layer 5 2.2227 0.5775
NEUROD2 Layer 4 2.7012 0.5762

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1934
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1934_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1934/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1934/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1934/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1934/report/PD/BN1934_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1934/report/PD/BN1934_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 09:46:43
  • Number of Processes: 10
  • Spending Time: 0h 3m